Can someone explain to me what clipping is? Should I always decode mpc's with clipping prevention on? If yes, why is it not actually the default? Does clipping occur with other encoder (mp3, aac, mp4, ogg...)?

Clipping happens when the amplitude of the signal of the original file you encode is higher than what's allowed by the CD Audio standard. This causes distortion which in extreme cases is audible.

You should *encode* MPCs with --xlevel, to allow for the encoder (the current ones like 1.14 and 1.15r) to handle those situations better. I don't know which program you use for decoding, but if you encoded properly (mppenc.exe --xlevel), there is not much more you can do (SV8 encoders of Musepack will handle it better without the need for any extra switch like --xlevel).

Each of the other formats has to deal with this phenomenon differently. The problem exists, but each codec handles it in its own way.